The first task, protein identification, is the easiest and has been automated nicely on several commercially available Time of Flight mass spectrometers. The FTMS offers better mass accuracy and hence better reliability in the identification.

The second task, peptide sequencing, is also relatively straightforward and is done routinely on quadrupole ion trap mass spectrometers. Again, the high performance of the FTMS will greatly simplify the data interpretation step and improve the reliability of this experiment.

The first step requires automation of the acquisition, peak picking, and database searching steps. The second, and later, tasks require automation of the MS^n experiment.

The third and fourth tasks are primarily computational projects. Once the automated mass spectrometer has generated the data, the computer must recognize that the protein identified has a modification, and automatically perform MS/MS or MS^n experiments to localize the modification.

As you can see, this project primarily involves a high degree of automation in the acquisition, sample stage control, and data analysis. The actual source has been built, but the automation requires a lot of work yet.